library(rmarkdown)
sdmApp is a R package containing a shiny application that allows non-expert R users to easily model species distribution. It offers a reproducible worklow for species distribution modelling into a single and user friendly environment. sdmApp takes raster data (in format supported by the raster package) and species occurrence data (several format supported) as input argument. the sdmApp provides an interactive, graphical user interface (GUI). This document will give an overview of the main functionalities of the graphical user interface. The main features of the GUI is:
Uploading data (raster and species occurence files)
View correlation between raster
Use Climate Ecological Niche Factors Analysis (CENFA) to select species predictors
Apply a spatial blocking for cross-validation (based on the blockCV package)
Apply species distribution models with or without a spatial blocking strategy
Export results
Keep reproducibility (R code) by being able do download the underlying code from sdmApp.
The GUI is build around 6 main windows, which can be selected from the navigation bar at the top of the screen. Initially, some of these windows will be empty and their content changes once data (both raster and species occurence files) have been uploaded.
This is the first page that is shown once the graphical user interface has been started using sdmApp() after loading package sdmApp. On this page, the user is presented the information about the package and contact or feedback.
On this page, the user can either upload both environmental and occurence data. The user has to upload first environnemental variable (rasters).You can also specify which variabe or raster is categorical.
Species occurence data (presence/absence format) files may be in CSV, Excel, SPSS, Stata or SAS format.
On this page, the user can :
view the summary on the occurrence data of the selected species and the rasters
view correlation (matrix and plot) between rasters
view species predictors by using Ecological Niche Factor Analysis (ENFA)
We note that the content of this page changes depending on whether data have already been uploaded or not.
We note that the content of this page changes depending on whether data have already been uploaded or not.